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Yorodumi- PDB-5t2v: Crystal structure of MSMEG_6753 a putative betaketoacyl-ACP reductase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t2v | |||||||||
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Title | Crystal structure of MSMEG_6753 a putative betaketoacyl-ACP reductase | |||||||||
Components | Oxidoreductase, short chain dehydrogenase/reductase family protein | |||||||||
Keywords | OXIDOREDUCTASE / FabG / mycobacterium / fatty acids | |||||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Oxidoreductase, short chain dehydrogenase/reductase family protein Function and homology information | |||||||||
Biological species | Mycobacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Blaise, M. / Van Wyk, N. / Baneres-Roquet, F. / Guerardel, Y. / Kremer, L. | |||||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Binding of NADP(+) triggers an open-to-closed transition in a mycobacterial FabG beta-ketoacyl-ACP reductase. Authors: Blaise, M. / Van Wyk, N. / Baneres-Roquet, F. / Guerardel, Y. / Kremer, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t2v.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t2v.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 5t2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/5t2v ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t2v | HTTPS FTP |
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-Related structure data
Related structure data | 5t2uC 4bnuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25604.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6753, MSMEI_6571 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R723 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M Hepes-Na pH 7.5, 30% peg400, 0.2M magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.9 Å / Num. obs: 17367 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rrim(I) all: 0.135 / Net I/σ(I): 11.27 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.21 / Rrim(I) all: 0.821 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BNU Resolution: 1.9→19.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.9 Å
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Refine LS restraints |
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LS refinement shell |
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